src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import MCview.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 \r
  27 public class AlignFrame extends GAlignFrame\r
  28 {\r
  29   final AlignmentPanel alignPanel;\r
  30   final AlignViewport viewport;\r
  31   public AlignFrame(AlignmentI al)\r
  32   {\r
  33     super();\r
  34     viewport = new AlignViewport(al,true,true,true,false);\r
  35     alignPanel = new AlignmentPanel(this, viewport);\r
  36     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  37     fontNameMenuItem.setText(viewport.getFont().getName());\r
  38     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  39   }\r
  40 \r
  41   protected void saveAs_actionPerformed(ActionEvent e)\r
  42   {\r
  43     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  44     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  45     chooser.setToolTipText("Save");\r
  46     int value = chooser.showSaveDialog(this);\r
  47     if(value == JFileChooser.APPROVE_OPTION)\r
  48     {\r
  49       String choice =  chooser.getSelectedFile().getPath();\r
  50       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  51       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  52       try{\r
  53         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  54         out.println(output);\r
  55         out.close();\r
  56       }\r
  57       catch(Exception ex){}\r
  58     }\r
  59 \r
  60   }\r
  61 \r
  62   protected void outputText_actionPerformed(ActionEvent e)\r
  63   {\r
  64      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  65      JInternalFrame frame = new JInternalFrame();\r
  66      cap.formatForOutput();\r
  67      frame.setContentPane(cap);\r
  68      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  69      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  70   }\r
  71 \r
  72   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  73   {\r
  74     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  75     htmlOutput = null;\r
  76   }\r
  77 \r
  78   public void printMenuItem_actionPerformed(ActionEvent e)\r
  79   {\r
  80     //Putting in a thread avoids Swing painting problems\r
  81     PrintThread thread = new PrintThread();\r
  82     thread.start();\r
  83   }\r
  84 \r
  85   class PrintThread extends Thread\r
  86   {\r
  87     public void run()\r
  88     {\r
  89       PrinterJob printJob = PrinterJob.getPrinterJob();\r
  90       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  91       printJob.setPrintable(alignPanel, pf);\r
  92       if (printJob.printDialog())\r
  93       {\r
  94         try\r
  95         {\r
  96           printJob.print();\r
  97         }\r
  98         catch (Exception PrintException)\r
  99         {\r
 100           PrintException.printStackTrace();\r
 101         }\r
 102       }\r
 103     }\r
 104 \r
 105   }\r
 106 \r
 107 \r
 108 \r
 109 \r
 110   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 111   {\r
 112     try{\r
 113       this.setClosed(true);\r
 114     }catch(Exception ex){}\r
 115   }\r
 116 \r
 117   ArrayList  historyList = new ArrayList();\r
 118   ArrayList redoList = new ArrayList();\r
 119 \r
 120   void updateEditMenuBar()\r
 121   {\r
 122     if(historyList.size()>0)\r
 123      {\r
 124        undoMenuItem.setEnabled(true);\r
 125        Object [] history = (Object[])historyList.get(0);\r
 126        undoMenuItem.setText("Undo "+history[0]);\r
 127      }\r
 128     else\r
 129     {\r
 130       undoMenuItem.setEnabled(false);\r
 131       undoMenuItem.setText("Undo");\r
 132     }\r
 133 \r
 134     if(redoList.size()>0)\r
 135      {\r
 136        redoMenuItem.setEnabled(true);\r
 137        Object [] history = (Object[])redoList.get(0);\r
 138        redoMenuItem.setText("Redo "+history[0]);\r
 139      }\r
 140     else\r
 141     {\r
 142       redoMenuItem.setEnabled(false);\r
 143       redoMenuItem.setText("Redo");\r
 144     }\r
 145   }\r
 146 \r
 147   public void addHistoryItem(String type)\r
 148   {\r
 149     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 150     redoList.clear();\r
 151     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 152     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 153     {\r
 154       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 155                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 156     }\r
 157 \r
 158     historyList.add(0, new Object[]{type,  seq} );\r
 159     updateEditMenuBar();\r
 160   }\r
 161 \r
 162   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 163   {\r
 164     Object [] history = (Object[])historyList.remove(0);\r
 165     // add the redo state before continuing!!\r
 166     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 167     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 168     {\r
 169       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 170                             viewport.getAlignment().getSequenceAt(i).\r
 171                             getSequence());\r
 172     }\r
 173     /////////\r
 174 \r
 175     redoList.add(0, new Object[] {history[0], seq});\r
 176 \r
 177       seq = (SequenceI[]) history[1];\r
 178       viewport.setAlignment( new Alignment(seq) );\r
 179       updateEditMenuBar();\r
 180       alignPanel.RefreshPanels();\r
 181   }\r
 182 \r
 183 \r
 184   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 185   {\r
 186      Object [] history = (Object[])redoList.remove(0);\r
 187      SequenceI[] seq = (SequenceI[]) history[1];\r
 188      viewport.setAlignment( new Alignment(seq) );\r
 189      updateEditMenuBar();\r
 190      alignPanel.RefreshPanels();\r
 191   }\r
 192 \r
 193 \r
 194   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 195   {\r
 196     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 197     JInternalFrame frame = new JInternalFrame();\r
 198     frame.setContentPane(geditor);\r
 199     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 200     frame.setResizable(false);\r
 201   }\r
 202 \r
 203 \r
 204   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 205   {\r
 206     Selection sel = viewport.getSelection();\r
 207     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 208       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 209     PaintRefresher.Refresh(null);\r
 210   }\r
 211 \r
 212   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 213   {\r
 214     viewport.getSelection().clear();\r
 215     PaintRefresher.Refresh(null);\r
 216   }\r
 217 \r
 218   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 219   {\r
 220     Selection sel = viewport.getSelection();\r
 221     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 222     {\r
 223       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 224         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 225       else\r
 226         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 227     }\r
 228     PaintRefresher.Refresh(null);\r
 229   }\r
 230 \r
 231 \r
 232   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 233   {\r
 234     viewport.getColumnSelection().clear();\r
 235     repaint();\r
 236   }\r
 237 \r
 238   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 239   {\r
 240     addHistoryItem("delete columns");\r
 241     ColumnSelection colSel = viewport.getColumnSelection();\r
 242     if (colSel.size() > 0)\r
 243     {\r
 244       int min = colSel.getMin();\r
 245       viewport.getAlignment().trimLeft(min);\r
 246       colSel.compensateForEdit(0,min);\r
 247       alignPanel.RefreshPanels();\r
 248     }\r
 249   }\r
 250 \r
 251   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 252   {\r
 253     addHistoryItem("delete columns");\r
 254     ColumnSelection colSel = viewport.getColumnSelection();\r
 255     if (colSel.size() > 0)\r
 256     {\r
 257       int max = colSel.getMax();\r
 258       if(max>1)\r
 259         viewport.getAlignment().trimRight(max);\r
 260 \r
 261       alignPanel.RefreshPanels();\r
 262     }\r
 263 \r
 264   }\r
 265 \r
 266   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 267   {\r
 268     addHistoryItem("delete gapped columns");\r
 269     viewport.getAlignment().removeGaps();\r
 270     alignPanel.RefreshPanels();\r
 271   }\r
 272 \r
 273   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 274   {\r
 275     addHistoryItem("delete all gaps");\r
 276     SequenceI current;\r
 277     int jSize;\r
 278     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 279     {\r
 280       current = viewport.getAlignment().getSequenceAt(i);\r
 281       jSize = current.getLength();\r
 282       for (int j=0; j < jSize; j++)\r
 283         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 284         {\r
 285           current.deleteCharAt(j);\r
 286           j--;\r
 287           jSize--;\r
 288         }\r
 289     }\r
 290 \r
 291     alignPanel.RefreshPanels();\r
 292   }\r
 293 \r
 294   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 295   {\r
 296     char thisChar = '-';\r
 297     char nextChar = '.';\r
 298     if(viewport.getGapCharacter()=='-')\r
 299     {\r
 300       thisChar = '.';\r
 301       nextChar = '-';\r
 302     }\r
 303     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 304     viewport.setGapCharacter(thisChar);\r
 305     alignPanel.RefreshPanels();\r
 306   }\r
 307 \r
 308   public void findMenuItem_actionPerformed(ActionEvent e)\r
 309   {\r
 310     JOptionPane op = new JOptionPane();\r
 311     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 312     Finder finder = new Finder(viewport, alignPanel, frame);\r
 313     frame.setContentPane(finder);\r
 314     frame.setSize(300,110);\r
 315     frame.setVisible(true);\r
 316   }\r
 317 \r
 318 \r
 319 \r
 320   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 321   {\r
 322     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 323 \r
 324 \r
 325     String selection = JOptionPane.showInternalInputDialog(this,\r
 326                                 "Select font",\r
 327                                 "Font selection",\r
 328                                 JOptionPane.QUESTION_MESSAGE,\r
 329                                 null,fonts\r
 330                                 ,fontNameMenuItem.getText()).toString();\r
 331     if(selection!=null)\r
 332     {\r
 333        fontNameMenuItem.setText(selection);\r
 334        SetFont();\r
 335      }\r
 336 \r
 337   }\r
 338 \r
 339   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 340   {\r
 341     String selection = JOptionPane.showInternalInputDialog(this,\r
 342                                 "Select font size",\r
 343                                 "Font size",\r
 344                                 JOptionPane.QUESTION_MESSAGE,\r
 345                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 346                                 ,fontSizeMenuItem.getText()).toString();\r
 347     if(selection!=null)\r
 348      {\r
 349        fontSizeMenuItem.setText(selection);\r
 350        SetFont();\r
 351      }\r
 352   }\r
 353 \r
 354   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 355   {\r
 356     String selection = JOptionPane.showInternalInputDialog(this,\r
 357                                 "Select font style",\r
 358                                 "Font style",\r
 359                                 JOptionPane.QUESTION_MESSAGE,\r
 360                                 null, new String[]{"plain", "bold", "italic"}\r
 361                                 ,fontStyleMenuItem.getText()).toString();\r
 362     if(selection!=null)\r
 363     {\r
 364       fontStyleMenuItem.setText(selection);\r
 365       SetFont();\r
 366     }\r
 367 \r
 368   }\r
 369 \r
 370   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 371   {\r
 372       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 373       alignPanel.RefreshPanels();\r
 374   }\r
 375 \r
 376   void SetFont()\r
 377   {\r
 378       int style = java.awt.Font.PLAIN;\r
 379       if(fontStyleMenuItem.getText().equals("bold"))\r
 380         style = java.awt.Font.BOLD;\r
 381       else if(fontStyleMenuItem.getText().equals("italic"))\r
 382         style = java.awt.Font.ITALIC;\r
 383 \r
 384       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 385                                            style,\r
 386                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 387       alignPanel.RefreshPanels();\r
 388 \r
 389   }\r
 390 \r
 391   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 392   {\r
 393     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 394     alignPanel.RefreshPanels();\r
 395   }\r
 396 \r
 397 \r
 398   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 399   {\r
 400     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 401     alignPanel.RefreshPanels();\r
 402   }\r
 403 \r
 404   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 405   {\r
 406     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 407     alignPanel.RefreshPanels();\r
 408   }\r
 409 \r
 410 \r
 411   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 412   {\r
 413     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 414     alignPanel.RefreshPanels();\r
 415   }\r
 416 \r
 417 \r
 418   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 419   {\r
 420     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 421   }\r
 422 \r
 423   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 424   {\r
 425 \r
 426     JInternalFrame frame = new JInternalFrame();\r
 427     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 428    try{\r
 429      overview = new OverviewPanel(alignPanel, viewport);\r
 430      frame.setContentPane(overview);\r
 431     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 432                              frame.getWidth(), frame.getHeight());\r
 433     frame.pack();\r
 434     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 435     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 436       {\r
 437             alignPanel.setOverviewPanel(null);\r
 438       };\r
 439     });\r
 440     alignPanel.setOverviewPanel( overview );\r
 441 \r
 442   }catch(java.lang.OutOfMemoryError ex)\r
 443    {\r
 444      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 445                                    +"\nTry reducing the font size.",\r
 446                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 447    }\r
 448 \r
 449 \r
 450   }\r
 451 \r
 452   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 453   {\r
 454     viewport.setGlobalColourScheme( null );\r
 455     changeColour();\r
 456   }\r
 457 \r
 458 \r
 459   public void clustalColour_actionPerformed(ActionEvent e)\r
 460   {\r
 461     viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
 462     changeColour();\r
 463   }\r
 464 \r
 465   public void zappoColour_actionPerformed(ActionEvent e)\r
 466   {\r
 467     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 468     changeColour();\r
 469   }\r
 470 \r
 471   public void taylorColour_actionPerformed(ActionEvent e)\r
 472   {\r
 473     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 474     changeColour();\r
 475   }\r
 476 \r
 477 \r
 478   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 479   {\r
 480     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 481     changeColour();\r
 482   }\r
 483 \r
 484   public void helixColour_actionPerformed(ActionEvent e)\r
 485   {\r
 486     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 487     changeColour();\r
 488   }\r
 489 \r
 490 \r
 491   public void strandColour_actionPerformed(ActionEvent e)\r
 492   {\r
 493     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 494     changeColour();\r
 495   }\r
 496 \r
 497 \r
 498   public void turnColour_actionPerformed(ActionEvent e)\r
 499   {\r
 500     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 501     changeColour();\r
 502   }\r
 503 \r
 504 \r
 505   public void buriedColour_actionPerformed(ActionEvent e)\r
 506   {\r
 507     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 508     changeColour();\r
 509   }\r
 510 \r
 511   void changeColour()\r
 512   {\r
 513     if(abovePIDThreshold.isSelected())\r
 514     {\r
 515       abovePIDThreshold_actionPerformed(null);\r
 516       alignPanel.setColourScheme( );\r
 517     }\r
 518     else if(conservationMenuItem.isSelected())\r
 519       conservationMenuItem_actionPerformed(null);\r
 520     else\r
 521       alignPanel.setColourScheme( );\r
 522 \r
 523   }\r
 524 \r
 525   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 526   {\r
 527     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 528 \r
 529     alignPanel.setColourScheme();\r
 530     ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 531 \r
 532     if(conservationMenuItem.isSelected())\r
 533     {\r
 534       if(sliderPanel!=null)\r
 535       {\r
 536         sliderPanel.cs = oldCs;\r
 537       }\r
 538 \r
 539       else\r
 540       {\r
 541         sliderPanel = new SliderPanel(alignPanel, 30, true,\r
 542                                       viewport.getGlobalColourScheme());\r
 543         JInternalFrame frame = new JInternalFrame();\r
 544         frame.setContentPane(sliderPanel);\r
 545         Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,\r
 546                                  90);\r
 547         frame.setMaximizable(false);\r
 548         frame.setResizable(false);\r
 549         frame.addInternalFrameListener(new javax.swing.event.\r
 550                                        InternalFrameAdapter()\r
 551         {\r
 552           public void internalFrameClosed(javax.swing.event.InternalFrameEvent\r
 553                                           evt)\r
 554           {\r
 555             sliderPanel = null;\r
 556           };\r
 557         });\r
 558       }\r
 559     }\r
 560     else\r
 561     {\r
 562         if(oldCs instanceof ConservationColourScheme)\r
 563         {\r
 564           ConservationColourScheme ccs = (ConservationColourScheme)oldCs;\r
 565           viewport.setGlobalColourScheme( ccs.cs );\r
 566         }\r
 567         alignPanel.setColourScheme();\r
 568     }\r
 569 \r
 570   }\r
 571 \r
 572   SliderPanel sliderPanel;\r
 573   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 574   {\r
 575     ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 576     int threshold = 0;\r
 577 \r
 578     if(abovePIDThreshold.isSelected())\r
 579     {\r
 580       if(sliderPanel!=null)\r
 581         sliderPanel.cs = oldCs;\r
 582 \r
 583       else\r
 584       {\r
 585         sliderPanel = new SliderPanel(alignPanel, 70, false, oldCs);\r
 586         JInternalFrame frame = new JInternalFrame();\r
 587         frame.setContentPane(sliderPanel);\r
 588         Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,\r
 589                                  90);\r
 590         frame.setMaximizable(false);\r
 591         frame.setResizable(false);\r
 592         frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 593         {\r
 594           public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 595           {\r
 596             sliderPanel = null;\r
 597           };\r
 598         });\r
 599 \r
 600       }\r
 601 \r
 602       threshold = sliderPanel.getValue();\r
 603     }\r
 604 \r
 605     if (oldCs instanceof ResidueColourScheme)\r
 606     {\r
 607       ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
 608       rcs.setThreshold(threshold);\r
 609     }\r
 610     else if (oldCs instanceof ScoreColourScheme)\r
 611     {\r
 612       ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
 613       scs.setThreshold(threshold);\r
 614     }\r
 615 \r
 616     alignPanel.setColourScheme();\r
 617 \r
 618   }\r
 619 \r
 620 \r
 621 \r
 622   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 623   {\r
 624     JInternalFrame frame = new JInternalFrame();\r
 625     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 626     frame.setContentPane(chooser);\r
 627     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 628     frame.setResizable(false);\r
 629     frame.setIconifiable(false);\r
 630     frame.setMaximizable(false);\r
 631   }\r
 632 \r
 633   public void PIDColour_actionPerformed(ActionEvent e)\r
 634   {\r
 635     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 636     alignPanel.setColourScheme( );\r
 637   }\r
 638 \r
 639 \r
 640   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 641   {\r
 642     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 643     alignPanel.setColourScheme();\r
 644   }\r
 645 \r
 646 \r
 647 \r
 648   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)\r
 649   {\r
 650     ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );\r
 651     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);\r
 652   }\r
 653 \r
 654 \r
 655   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 656   {\r
 657     addHistoryItem("sort");\r
 658     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 659     alignPanel.RefreshPanels();\r
 660   }\r
 661 \r
 662   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 663   {\r
 664     addHistoryItem("sort");\r
 665     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 666     alignPanel.RefreshPanels();\r
 667   }\r
 668 \r
 669   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 670   {\r
 671     addHistoryItem("sort");\r
 672     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 673     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 674     alignPanel.RefreshPanels();\r
 675   }\r
 676 \r
 677   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 678   {\r
 679     addHistoryItem("sort");\r
 680     if(viewport.getCurrentTree()==null)\r
 681       return;\r
 682 \r
 683     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 684     alignPanel.RefreshPanels();\r
 685   }\r
 686 \r
 687   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 688   {\r
 689     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 690     JInternalFrame frame = new JInternalFrame();\r
 691     frame.setContentPane(sp);\r
 692     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 693     frame.setMaximizable(false);\r
 694     frame.setResizable(false);\r
 695 \r
 696   }\r
 697 \r
 698   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 699   {\r
 700     if(viewport.getSelection().size()<2)\r
 701       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 702     else\r
 703     {\r
 704       JInternalFrame frame = new JInternalFrame();\r
 705       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 706       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 707     }\r
 708   }\r
 709 \r
 710   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 711   {\r
 712     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 713        || viewport.getAlignment().getHeight()<4)\r
 714     {\r
 715       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 716                                     +"at least 4 input sequences.",\r
 717                                     "Sequence selection insufficient",\r
 718                                     JOptionPane.WARNING_MESSAGE);\r
 719       return;\r
 720     }\r
 721 \r
 722     try{\r
 723       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 724       JInternalFrame frame = new JInternalFrame();\r
 725       frame.setContentPane(pcaPanel);\r
 726       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 727    }catch(java.lang.OutOfMemoryError ex)\r
 728    {\r
 729      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 730                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 731    }\r
 732 \r
 733 \r
 734   }\r
 735 \r
 736   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 737   {\r
 738     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 739   }\r
 740 \r
 741   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 742   {\r
 743     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 744   }\r
 745 \r
 746 \r
 747   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 748   {\r
 749     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 750   }\r
 751 \r
 752   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 753   {\r
 754     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 755   }\r
 756 \r
 757   void NewTreePanel(String type, String pwType, String title)\r
 758   {\r
 759     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 760     TreePanel tp=null;\r
 761    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 762    {\r
 763      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 764                          viewport.getStartRes(), viewport.getEndRes());\r
 765    }\r
 766    else\r
 767    {\r
 768      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 769                          type, pwType, viewport.getStartRes(),\r
 770                          viewport.getEndRes());\r
 771    }\r
 772 \r
 773    frame.setContentPane(tp);\r
 774    Desktop.addInternalFrame(frame, title, 600, 500);\r
 775   }\r
 776 \r
 777 \r
 778 \r
 779   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781     JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"\r
 782                                   +"\nwithin the Barton Group, Dundee University."\r
 783                                   +"\nThis will be available as a web service 2005",\r
 784                                   "Web service", JOptionPane.INFORMATION_MESSAGE);\r
 785   }\r
 786 \r
 787   public void pdbTest_actionPerformed(ActionEvent e)\r
 788   {\r
 789    String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 790 \r
 791    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 792    if (reply.length()>1)\r
 793      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 794 \r
 795    try\r
 796    {\r
 797      PDBfile pdb = new PDBfile(url,\r
 798                                "URL");\r
 799     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 800     seq.setPDBfile(pdb);\r
 801      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 802      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 803   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 804 \r
 805      rotCanvas rc = new rotCanvas(pdb);\r
 806      JInternalFrame frame = new JInternalFrame();\r
 807      frame.setContentPane(rc);\r
 808      Desktop.addInternalFrame(frame, url, 400,400);\r
 809    }\r
 810    catch (Exception ex)\r
 811    {\r
 812      ex.printStackTrace();\r
 813    }\r
 814 \r
 815   }\r
 816 \r
 817 \r
 818   public void doKeyPressed(KeyEvent evt)\r
 819   {\r
 820 \r
 821     System.out.println(evt.getKeyChar());\r
 822     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 823       findMenuItem_actionPerformed(null);\r
 824 \r
 825   }\r
 826 \r
 827 \r
 828 }\r